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- PDB-9hta: Dispersin from Terribacillus saccharophilus Dispts2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9hta
TitleDispersin from Terribacillus saccharophilus Dispts2 in complex with NAG-thiazoline
ComponentsDispersin
KeywordsHYDROLASE / biofilm degradation / GH20 / poly-N-acetylglucosamine / enzyme catalysis
Function / homologyChem-NGT
Function and homology information
Biological speciesTerribacillus saccharophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsMales, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. ...Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / Franco Cairo, J.P.L. / Pache, R.A. / Vejborg, R.M. / Bhosale, S. / Vocadlo, D. / Davies, G.J. / Wilson, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Expansion of the diversity of dispersin scaffolds.
Authors: Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / ...Authors: Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / Franco Cairo, J.P.L. / Nitz, M. / Pache, R.A. / Vejborg, R.M. / Bhosale, S. / Vocadlo, D.J. / Davies, G.J. / Wilson, K.S.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dispersin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7812
Polymers37,5621
Non-polymers2191
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint2 kcal/mol
Surface area13190 Å2
Unit cell
Length a, b, c (Å)90.06, 90.06, 98.12
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dispersin


Mass: 37562.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Terribacillus saccharophilus (bacteria)
Production host: Bacillus subtilis (bacteria)
#2: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MPD screen E7: 0.1 M Citric acid pH 4.0, 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.17→40.93 Å / Num. obs: 23157 / % possible obs: 93.1 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.099 / Χ2: 1.03 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.95-40.9310.30.04138.54000.9990.0180.0450.6698.6
2.17-2.2411.24.7350.516240.5322.1515.211.0376.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→40.926 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.311 / SU ML: 0.172 / Cross valid method: FREE R-VALUE / ESU R: 0.235 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2528 1089 4.721 %
Rwork0.2121 21976 -
all0.214 --
obs-23065 92.895 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.004 Å2
Baniso -1Baniso -2Baniso -3
1-0.595 Å20.298 Å2-0 Å2
2--0.595 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.17→40.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 14 43 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122708
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162384
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.8053684
X-RAY DIFFRACTIONr_angle_other_deg0.5641.7515510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9945322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.53356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.610447
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.53610146
X-RAY DIFFRACTIONr_chiral_restr0.0690.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023183
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02629
X-RAY DIFFRACTIONr_nbd_refined0.2070.2536
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.22281
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0510.27
X-RAY DIFFRACTIONr_nbd_other0.1460.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.24
X-RAY DIFFRACTIONr_mcbond_it4.6425.7921291
X-RAY DIFFRACTIONr_mcbond_other4.6415.7911292
X-RAY DIFFRACTIONr_mcangle_it6.43210.4031612
X-RAY DIFFRACTIONr_mcangle_other6.4310.4011613
X-RAY DIFFRACTIONr_scbond_it4.5686.1371417
X-RAY DIFFRACTIONr_scbond_other4.5646.141415
X-RAY DIFFRACTIONr_scangle_it6.97811.1232072
X-RAY DIFFRACTIONr_scangle_other6.97611.1232073
X-RAY DIFFRACTIONr_lrange_it9.21569.60911952
X-RAY DIFFRACTIONr_lrange_other9.21569.61511946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.17-2.2260.372780.38715100.38718230.8860.91287.10920.393
2.226-2.2870.842170.7373100.74417540.6430.69718.64310.823
2.287-2.3530.36910.3515970.3517030.8780.91499.11920.335
2.353-2.4250.337790.30116010.30316820.9260.9499.88110.28
2.425-2.5050.263620.2715540.2716160.9620.9521000.248
2.505-2.5920.393660.24514800.2515460.9150.9621000.22
2.592-2.690.27660.22114410.22315070.9470.9681000.195
2.69-2.7990.256710.23913950.2414660.9540.9631000.212
2.799-2.9230.299610.23113430.23414040.950.9661000.208
2.923-3.0650.297430.21312940.21513370.9530.971000.196
3.065-3.230.232550.22612160.22612710.9610.9661000.213
3.23-3.4240.276640.21711510.2212190.9550.96899.67190.205
3.424-3.6590.33570.23810450.24211370.9390.96296.92170.223
3.659-3.9490.288500.2899880.28910720.9350.93596.82840.257
3.949-4.3220.183330.1649570.1659940.9840.98499.59760.172
4.322-4.8260.165490.1388530.1399020.9820.9891000.15
4.826-5.5590.193350.157740.1528090.9810.9881000.162
5.559-6.7770.223430.1846430.1866860.970.981000.194
6.777-9.4560.196410.1435040.1475450.9740.9861000.16
9.456-40.9260.265280.2223200.2263500.9530.9699.42860.24

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